[IR] Fix Module::setModuleFlag for uniqued metadata (#164580) `Module::setModuleFlag` is supposed to change a single module. However, when an `MDNode` has the same value in more than one module in the same `LLVMContext`, such `MDNode` is shared (uniqued) across all of them. Therefore `MDNode::replaceOperandWith` changes all modules that share the same `MDNode`. This used to cause problems for #86212, where a module is marked as "upgraded" via a module flag. When this flag is shared across multiple modules, all of them are marked, yet some may not have been processed at all. After the patch we now construct a new `MDNode` and replace the old one.
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